15-83018146-A-G

Variant names:

• chr15-83018146-A-G
• rs2032208489
• NM_025238.4:c.1370T>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_025238.4(BTBD1):​c.1370T>C​(p.Phe457Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BTBD1 NM_025238.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.850

Genes affected

BTBD1 (HGNC:1120): (BTB domain containing 1) The C-terminus of the protein encoded by this gene binds topoisomerase I. The N-terminus contains a proline-rich region and a BTB/POZ domain (broad-complex, Tramtrack and bric a brac/Pox virus and Zinc finger), both of which are typically involved in protein-protein interactions. Subcellularly, the protein localizes to cytoplasmic bodies. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ENSG00000259805 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17477319).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD1	NM_025238.4	c.1370T>C	p.Phe457Ser	missense_variant	Exon 8 of 8	ENST00000261721.9	NP_079514.1
BTBD1	NM_001011885.2	c.*124T>C		3_prime_UTR_variant	Exon 7 of 7		NP_001011885.1
LOC124903542	XR_007064742.1	n.1319+5087A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD1	ENST00000261721.9	c.1370T>C	p.Phe457Ser	missense_variant	Exon 8 of 8	1	NM_025238.4	ENSP00000261721.4
BTBD1	ENST00000379403	c.*124T>C		3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000368713.2
ENSG00000259805	ENST00000566841.1	n.735-85278A>G		intron_variant	Intron 1 of 1	5
ENSG00000260608	ENST00000570202.1	n.62+5424A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000468 Hom.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Oct 05, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1370T>C (p.F457S) alteration is located in exon 8 (coding exon 8) of the BTBD1 gene. This alteration results from a T to C substitution at nucleotide position 1370, causing the phenylalanine (F) at amino acid position 457 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	18
DANN	Benign	0.95
DEOGEN2	Benign	0.021	T
Eigen	Benign	-0.17
Eigen_PC	Benign	0.032
FATHMM_MKL	Benign	0.75	D
LIST_S2	Benign	0.60	T
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.17	T
MetaSVM	Benign	-0.80	T
MutationAssessor	Benign	0.34	N
PrimateAI	Benign	0.44	T
PROVEAN	Benign	1.7	N
REVEL	Benign	0.12
Sift	Benign	0.40	T
Sift4G	Benign	0.41	T
Polyphen		0.0090	B
Vest4		0.11
MutPred		0.61		Gain of disorder (P = 0.0066);
MVP		0.78
MPC		0.90
ClinPred		0.20	T
GERP RS		4.6
Varity_R		0.057
gMVP		0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2032208489; hg19: chr15-83686898;